Nextstrain

Name: Nextstrain · GitHub
Rating: 4.7 (2138 reviews)

Real-time tracking of pathogen evolution

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ncovncovPublic
Nextstrain build for SARS-CoV-2
Python 1.4k 406
auguraugurPublic
Pipeline components for real-time phylodynamic analysis
Python 269 131
auspiceauspicePublic
Web app for visualizing pathogen evolution
JavaScript 300 166

Repositories

docker-base Public
Docker image build for nextstrain/base
nextstrain/docker-base’s past year of commit activity
Shell 12 6 12 5 Updated Apr 26, 2025
nextclade Public
Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
nextstrain/nextclade’s past year of commit activity
Rust 229MIT 61 111 (31 issues need help) 20 Updated Apr 26, 2025
seasonal-flu Public
Scripts. config, and snakefiles for seasonal-flu nextstrain builds
nextstrain/seasonal-flu’s past year of commit activity
Python 49 28 27 5 Updated Apr 26, 2025
forecasts-ncov Public
SARS-CoV-2 variant growth rates and frequency forecasts
nextstrain/forecasts-ncov’s past year of commit activity
Python 7 2 11 4 Updated Apr 25, 2025
nextstrain.org Public
The Nextstrain website
nextstrain/nextstrain.org’s past year of commit activity
JavaScript 96AGPL-3.0 50 73 15 Updated Apr 25, 2025
augur Public
Pipeline components for real-time phylodynamic analysis
nextstrain/augur’s past year of commit activity
Python 269AGPL-3.0 131 221 (1 issue needs help) 37 Updated Apr 25, 2025
cli Public
The Nextstrain command-line interface (CLI)—a program called nextstrain—which aims to provide a consistent way to run and visualize pathogen builds and access Nextstrain components like Augur and Auspice across computing environments such as Docker, Conda, and AWS Batch.
nextstrain/cli’s past year of commit activity
Python 27MIT 20 67 5 Updated Apr 25, 2025
conda-base Public
Conda package build for nextstrain-base
nextstrain/conda-base’s past year of commit activity
Shell 1 1 9 4 Updated Apr 25, 2025
nextstrain-walkthrough Public
Workshop for VEME 2022: Real-time tracking of pathogen evolution using Nextstrain
nextstrain/nextstrain-walkthrough’s past year of commit activity
4MIT 1 0 0 Updated Apr 25, 2025
nextclade_data Public
Datasets for https://github.com/nextstrain/nextclade
nextstrain/nextclade_data’s past year of commit activity
Python 33 28 9 15 Updated Apr 25, 2025